- phenixbb - phenix-online.org

Macromolecular Crystallography - CSHL Course October 2024
by Paul Adams 07 Mar '24

07 Mar '24

Dear Colleagues, The Cold Spring Harbor Macromolecular Crystallography course will take place October 13-29th this year (pleased see below for more details). This comprehensive course is an outstanding place to learn both the theoretical and practical aspects of macromolecular crystallography. There are extensive lectures and practical sessions from world recognized experts in crystallization, data collection, data processing, structure solution, refinement, and validation. The goal of the course is for researchers who have had some exposure to structural biology to become experts in crystallography. This is an experience in macromolecular crystallography learning that cannot be found anywhere else, and the student/teacher ratio is often 1:1. Please follow the link below to the course web site. In particular, please note the information about the various fellowships, scholarships, and stipends that are available. If anyone has any questions please send me an e-mail, and we will be happy to answer all queries. Paul Adams <https://r20.rs6.net/tn.jsp?f=001fnNri6rmFxDJaH0HgFMkV8PNwKevLhjwrpcpWrfCqoq…> <https://r20.rs6.net/tn.jsp?f=001fnNri6rmFxDJaH0HgFMkV8PNwKevLhjwrpcpWrfCqoq…> Macromolecular Crystallography <https://r20.rs6.net/tn.jsp?f=001fnNri6rmFxDJaH0HgFMkV8PNwKevLhjwrpcpWrfCqoq…> October 13 - 29, 2024 Applications Due: July 15 Instructors Paul Adams, Lawrence Berkeley National Laboratory Dorothee Liebschner, Lawrence Berkeley National Laboratory Janet Newman, UNSW, Australia James Pflugrath, Rigaku Americas Corporation (ret.), Texas Co-Instructor Tom Peat, UNSW, Australia Topics Covered Basic Diffraction Theory Structure Presentation Coordinate Deposition Structure Validation Model Building and Refinement Electron Density Maps Improvement Using Predicted Models in Structure Solution and Completion Protein Structure Prediction Structure Solution by Experimental Phasing Methods (SAD, MAD, MIR, and others) and Molecular Replacement Data Collection and Processing Synchrotron X-ray Sources and Optics Crystallization (Proteins, Nucleic Acids, Complexes and Membrane Proteins) For further information and to apply please visit the Macromolecular Crystallography course website. <https://r20.rs6.net/tn.jsp?f=001fnNri6rmFxDJaH0HgFMkV8PNwKevLhjwrpcpWrfCqoq…> Cold Spring Harbor Laboratory - Meetings & Courses | 1 Bungtown Road, Cold Spring Harbor, NY 11724 -- Paul Adams (he/him/his) Associate Laboratory Director for Biosciences, LBL (https://biosciences.lbl.gov) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, UC Berkeley (http://bioeng.berkeley.edu) Member of the Graduate Group in Comparative Biochemistry, UC Berkeley (http://compbiochem.berkeley.edu) Building 91, Room 410 Building 978, Room 4126 Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: 0000-0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 91R0183 Berkeley, CA 94720, USA. Executive Assistant: Michael Espinosa [ MEEspinosa(a)lbl.gov ][ 1-510-333-6788 ] Phenix Consortium: Ashley Dawn [ AshleyDawn(a)lbl.gov ][ 1-510-486-5455 ] --

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map display after resolve_cryoem
by Valerie Biou 01 Mar '24

01 Mar '24

Hello, I ran resolve_cryoem for solvent flattening and obtained a ccp4 map that behaves like a mask both in Coot and Chimera. the histogram is just a single line and the dimensions are different from my original map, even though in a second run I used restore_full_size = true in a second run. To be clear, my original map has 480^3 dimensions, and the output one is 125x140x224, which boxes my protein but I can't see the inside of the map. I guess there is something I didn't understand. Can you please help me? All the best, Valerie Valérie Biou, Ph.D. valerie.biou(a)ibpc.fr Laboratoire de Biologie Physico-Chimique des Protéines Membranaires umr7099.ibpc.fr <http://umr7099.ibpc.fr/> UMR 7099 CNRS/Univ. Paris-Cité Institut de Biologie Physico-Chimique 13 rue Pierre et Marie Curie 75005 Paris - France Tel : +33 (0)1 5841 5099

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Re: [phenixbb] Joint X-ray / neutron refinement
by Kristoffer Lundgren 24 Feb '24

24 Feb '24

Hello phenixbb, When trying to do joint refinement in phenix.refine 1.21-5207 using the suggested joint_xn.eff file found at https://phenix-online.org/documentation/reference/refinement.html#neutron-a… as a template I get some error messages (running phenix.refine from the command line): Unrecognized PHIL parameters: ----------------------------- xray.refinement.refine.strategy (file "joint_xn.eff", line 33) xray.refinement.main.simulated_annealing (file "joint_xn.eff", line 36) xray.refinement.main.ordered_solvent (file "joint_xn.eff", line 37) xray.refinement.main.number_of_macro_cycles (file "joint_xn.eff", line 38) neutron.refinement.refine.strategy (file "joint_xn.eff", line 45) neutron.refinement.main.simulated_annealing (file "joint_xn.eff", line 48) neutron.refinement.main.ordered_solvent (file "joint_xn.eff", line 49) neutron.refinement.main.number_of_macro_cycles (file "joint_xn.eff", line 50) Can you please advice on how to proceed? It looks like the options supplied are not recognized at all by phenix.refine. Best regards Kristoffer From: <phenixbb-bounces(a)phenix-online.org> on behalf of Derek Logan <derek.logan(a)biochemistry.lu.se> Date: Monday, 22 January 2024 at 09:39 To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Cc: Ulf Ryde <ulf.ryde(a)compchem.lu.se>, "esko.oksanen_ess.eu" <esko.oksanen(a)ess.eu> Subject: ***SPAM*** [phenixbb] Joint X-ray / neutron refinement Hi phenixbb, I'm trying to understand the current status of joint X-ray/neutron refinement in phenix.refine. The announcement of the latest release mentions a change in the algorithm as described in the recent publication. In the documentation: Structure refinement in PHENIX<https://phenix-online.org/documentation/reference/refinement.html#neutron-a…> phenix-online.org<https://phenix-online.org/documentation/reference/refinement.html#neutron-a…> [AURqZhI53yp3gAAAABJRU5ErkJggg==]<https://phenix-online.org/documentation/reference/refinement.html#neutron-a…> it's described how you can run joint refinement using a parameter file. Does this mean that it is *only* possible in this way and not through the GUI? The GUI was very useful in the past as it automatically opened Coot with the maps for both X-rays and neutrons, and the refinement statistics for both were displayed in the GUI. As far as I can see joint refinement via the GUI last worked in version 1.19.2-4148 from 2021. Best regards Derek

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Rotamer error in real space refinement
by Nikos Pinotsis 24 Feb '24

24 Feb '24

Hi, I am using real space refine with the latest phenix 1.21-5207 for fitting a model into a cryoEM map. During refiment one Trp goes clearly out of density (vertical to the density) although the map is very well defined at this part of the protein. I tried local_grid_search either for every cycle or last, however it didn't fix the problem. I know that this is reported a couple of years ago as fixed (dev-4218), I am wondering if something changed during the last version. Another solution I can think it to keep the side chain of this Trp fixed. How can I do that? thanks Nikos -- ________________________________________ Nikos Pinotsis Associate Professor Biochemistry, Department of Chemistry National and Kapodistrian University of Athens

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Define bond between O3' of a nucleotide to P of 3DR HETATM ligand (abasic nucleotide)
by Mark Saper 24 Feb '24

24 Feb '24

I need to create a phosphodiester bond between O3’ of a DNA nucleotide and P of a 3DR HETATM ligand (a modified nucleotide). I also need to delete O3P of the 3DR nucleotide. How can I create this restraint? Also, how can I get COOT to display this bond? Thanks, Mark _____________________ Mark A. Saper, Ph.D. Dept of Microbiology and Molecular Genetics Hebrew University Faculty of Medicine saper(a)umich.edu <mailto:[email protected]> | +972 52 815-0480

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Tenure track position in Protein Science for Pathogen Defense
by Cygler, Miroslaw 21 Feb '24

21 Feb '24

Dear Colleagues, I am excited to let you know that the Department of Biochemistry, Microbiology and Immunology, College of Medicine, University of Saskatchewan, is searching for an exceptional candidate in the area of Protein Science for Pathogen Defense, to fill a tenure-track Canada Research Chair (CRC) Tier 2 position. The CRC program is the flagship of a national strategy to make Canada one of the world's top countries in research and development. We are looking for an outstanding early career scientist to establish and lead a groundbreaking research program in protein science to understand the mechanisms of bacterial and viral infection in humans or animals, to investigate host-pathogen interactions, or to discover novel mechanisms of defense against known and potential future pathogens. Within this broad scope, specific areas of interest include synthetic antigen design, the molecular basis of immune response to pathogens, mechanisms of antimicrobial resistance, and the prediction-guided design of artificial antibodies. We are interested in hiring a world-class expert in one or more of the following areas: (i) protein structure prediction and structural bioinformatics, (ii) protein design, and (iii) cryo-electron microscopy. A detailed advertisement with instruction how to apply is enclosed and can also be viewed here: <https://usask.csod.com/ux/ats/careersite/14/home/requisition/12015?c=usask&…> Canada Research Chair (CRC) Tier 2 in Protein Science for Pathogen Defense<https://usask.csod.com/ux/ats/careersite/14/home/requisition/12015?c=usask&…> protection.outlook.com<https://usask.csod.com/ux/ats/careersite/14/home/requisition/12015?c=usask&…> [X]<https://usask.csod.com/ux/ats/careersite/14/home/requisition/12015?c=usask&…> . Regards, Mirek ======================================================= Dr. Miroslaw Cygler, FCAHS Professor, Dept. Biochem, Microbiol & Immune, U. of Saskatchewan Canada Research Chair in Molecular Medicine Using Synchrotron Light Health Sciences Building 3D30.6 (Box 9) 107 Wiggins Road, Saskatoon, SK S7N 5E5 Canada Email: miroslaw.cygler(a)usask.ca<mailto:[email protected]> Website: http://research-groups.usask.ca/cyglerlab/ Phone: 306-966-4361, cell: 306-203-2317 =======================================================

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Structural Biology Workshop, June 10-12, 2024, Arlington, VA
by Meilleur, Flora 16 Feb '24

16 Feb '24

Dear All, We would like to bring to your attention the 2024 Neutrons in Structural Biology workshop. This workshop will highlight the need for next-generation instruments and toolsets for structural biology, with a focus on neutrons and other complementary techniques, and the development of integrated experimental and computational frameworks that connect them. Neutrons in Structural Biology - Challenges & Opportunities June 10-12th 2024 Sheraton Pentagon City Hotel, Arlington, VA. For details and registration see: Neutrons in Structural Biology - Challenges & Opportunities<https://conference.sns.gov/event/402/> The workshop will include a 1-day satellite training workshop (June 10, 2024) to educate graduate students and postdoctoral researchers in the application of neutron techniques in structural biology. A limited numbers of travel awards are available to support graduate students and post-doctoral fellows attendance at the workshop. The travel award application deadline is April 12, 2024. Details here<https://conference.sns.gov/event/402/page/2891-travel-awards-deadline-april…>. Flora Meilleur on behalf of the organizing committee: Andrey Kovalevsky Flora Meilleur Dean Myles Hugh O'Neill Flora Meilleur, Ph.D. Neutron Scattering Scientist Neutron Sciences Directorate Oak Ridge National Laboratory Professor Molecular & Structural Biochemistry N C State University Editor, Journal of Applied Crystallography Office: 865-576-2779

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to leave atoms out of ADP restraints
by Jorge Iulek 14 Feb '24

14 Feb '24

Hi, all, The ADP restraints I refer to in this discussion are the ones that would make B-factors of nearby atoms to influence (or more or less resemble) each other. For some very disordered side chains, I would like to test "taking out" the "more disordered" atoms (maybe for high chi angle variability) of these restraints, for them to be more free to skyrocket, but also that they do not influence so much the main chain, in some cases where the flexibility difference between main and side chain seems to be significant. Is there a way to do so? Thanks, Jorge

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helical structure - Real space refinement
by Dmitry Semchonok 02 Feb '24

02 Feb '24

Dear colleagues, Is there any specific procedure for Real space refinement in Phenix, having a map and model when working with helical structure? Many thanks Kind regard, Dmitry

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RealSpaceRefine Nucleic acid SS restraints ?
by CUNIASSE Philippe 01 Feb '24

01 Feb '24

Dear all, I am currently refining a protein-nucleic acid structure obtained by MDFF (NAMD) with a 2.9 Å cryo-EM map. Dues to the poor density of the map at the end of the DNA duplex (likely due to breathing at the ends of the duplex), the structure of the DNA tends to be distorted. I tried to set up a set of nucleic acid restraints (Base pairing and base stacking for the full sequence), however, despite the fact that the syntax was checked and no error message is present in the log file, it seems that the restraints are not taken into account as if the constant restraints were two weak. And indeed when examining the refined structure, the pairing and stacking restraints for the base pairs at the extremities of the DNA duplex are not fulfilled. Have you a suggestion to solve this problem ? Thanks in advance for your help. Best regards. Philippe. ----------------------------------------------- Philippe Cuniasse, PhD/HDR. Institute for Integrative Biology of the Cell (I2BC) UMR 9198 CNRS-CEA-Univ Paris Sud Bat 144 CE-Saclay 91191 Gif-sur-Yvette Cedex, France Tel: (33) 1 69 08 56 35 Fax: (33) 1 69 08 47 12 Email: philippe.cuniasse(a)cea.fr<mailto:[email protected]> Web: http://biodev.cea.fr/rasmot3d/ Web: https://www.i2bc.paris-saclay.fr [signature_2602492259]

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leave residue inside its electron density when neighbor is too close
by Murpholino Peligro 29 Jan '24

29 Jan '24

What is the recommended approach to tell phenix.refine to leave the residue inside its electron density? (crystal neighbors) The green model is the input to phenix.refine, the maps and the yellow model are the output of phenix.refine. As you can see, phenix.refine will move the residue outside the density (to avoid clashes I guess?) I have tried setting the occupancy of OXT to 0.5, but it is not good. (you can see there is a water in a special position, just above the bad residue) Any more ideas?

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phenix.mtriage output model-map
by joe.wilson2023 23 Jan '24

23 Jan '24

Dear Phenix team, I am new to Phenix and using the phenix.mtriage to get the map-model FSC results. It gives the correct results at the same time I also want to produce the mode-map used for the FSC calculation. Is there an option for this? If not how can I reproduce the same model-map with another phenix command? Many thanks, Joe

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ResolveCryoEM problem
by Luca Pellegrini 23 Jan '24

23 Jan '24

Hi, I am trying to run Resolve with two half maps and a sequence file with ncs copies of the sequence. Resolve stops with the message: “Need a symmetry file if ncs_copies > 1 and using models”. But I am not using models. Please advise. Regards, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA UK

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Joint X-ray / neutron refinement
by Derek Logan 22 Jan '24

22 Jan '24

Hi phenixbb, I'm trying to understand the current status of joint X-ray/neutron refinement in phenix.refine. The announcement of the latest release mentions a change in the algorithm as described in the recent publication. In the documentation: <https://phenix-online.org/documentation/reference/refinement.html#neutron-a…> Structure refinement in PHENIX<https://phenix-online.org/documentation/reference/refinement.html#neutron-a…> phenix-online.org<https://phenix-online.org/documentation/reference/refinement.html#neutron-a…> [X] <https://phenix-online.org/documentation/reference/refinement.html#neutron-a…> it's described how you can run joint refinement using a parameter file. Does this mean that it is *only* possible in this way and not through the GUI? The GUI was very useful in the past as it automatically opened Coot with the maps for both X-rays and neutrons, and the refinement statistics for both were displayed in the GUI. As far as I can see joint refinement via the GUI last worked in version 1.19.2-4148 from 2021. Best regards Derek

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treating the water molecules in the model
by Dmitry Semchonok 20 Jan '24

20 Jan '24

Dear colleagues, Please share your experience with how you handle the water molecules. So, we have a refined model and added the water molecules using the Douse protocol. So, should we refine the model again afterwards? Or is the model considered ready? We tried to refine our model with water, but then the water molecules flew away from the places. Please let me know what is the correct way to proceed. Many thanks for considering my request. Sincerely, Dmitry

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General interest: Interoperability of crystallographic data and databases
by John R Helliwell 19 Jan '24

19 Jan '24

Dear Colleagues, I imagine you will be interested in this Feature Article on the "Interoperability of crystallographic data and databases" in the current issue of IUCrJ:- https://journals.iucr.org/m/issues/2024/01/00/lt5064/index.html Best wishes, John Emeritus Professor John R Helliwell DSc

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Post to the email list
by Supeshala Nawarathnage 19 Jan '24

19 Jan '24

Hello, I would like to request to add my email address to your mailing list. My email address is nawa.science(a)gmail.com Thank you. Sincerely, Supeshala Nawarathnage

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Updated links - Phenix version 1.21 released
by Paul Adams 19 Jan '24

19 Jan '24

The Phenix developers are pleased to announce that version 1.21 of Phenix is now available (build 1.21-5207). Binary installers for Linux, Mac OSX, and Windows (under Windows Subsystem for Linux), and the source installer, are available at the download site: http://phenix-online.org/download Highlights for the 1.21 version of Phenix include: - Likelihood-based docking of models into cryo-EM maps. • Full support for structure determination with AlphaFold models. • New joint X-ray and neutron refinement algorithm. • Quantum Mechanical Restraints (QMR) to calculate ligand restraints in situ. Detailed changes are: - Full support for structure determination with AlphaFold models in Phenix GUI - PredictAndBuild X-ray and Cryo-EM structure solution from data and sequences - Phenix AlphaFold server - Video tutorials for prediction, X-ray structure solution and Cryo-EM map interpretation - Cryo-EM tools support ChimeraX visualization - Cryo-EM density modification and anisotropic scaling display local resolution - Tutorials available for automated structure determination with PredictAndBuild - New em_placement and emplace_local tools - likelihood-based docking of models into cryo-EM maps - MOPAC v22 is now distributed with Phenix - Quantum Mechanical Restraints (QMR) to calculate ligand restraints in situ - Available in phenix.refine and separate command-line tool, mmtbx.quantum_interface - Defaults to MOPAC's PM6-D3H4 - Higher level QM available via 3rd-party Orca package - Restraints - Approximately 27k of 37k restraints (QM calculated and validated) deployed in the GeoStd - Automated tests for programs in the Phenix GUI - ERRASER no longer supported and removed from installation - Remove rebuild_predicted_model (duplicated by predict_and_build) - JSON output added to MolProbity structure validation scripts Please note that this publication should be used to cite the use of Phenix: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD: Acta Cryst. (2019). D75, 861-877. https://doi.org/10.1107/S2059798319011471 Full documentation is available here: http://www.phenix-online.org/documentation There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. The maintenance and distribution of Phenix is funded by the National Institute of General Medical Sciences (NIH) under grant R24-GM141254. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams (he/him/his) Associate Laboratory Director for Biosciences, LBL (https://biosciences.lbl.gov) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, UC Berkeley (http://bioeng.berkeley.edu) Member of the Graduate Group in Comparative Biochemistry, UC Berkeley (http://compbiochem.berkeley.edu) Building 91, Room 410 Building 978, Room 4126 Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: 0000-0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 91R0183 Berkeley, CA 94720, USA. Executive Assistant: Michael Espinosa [ MEEspinosa(a)lbl.gov ][ 1-510-333-6788 ] Phenix Consortium: Ashley Dawn [ AshleyDawn(a)lbl.gov ][ 1-510-486-5455 ] --

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Phenix version 1.21 released
by Paul Adams 18 Jan '24

18 Jan '24

The Phenix developers are pleased to announce that version 1.21 of Phenix is now available (build 1.21-5207). Binary installers for Linux, Mac OSX, and Windows (under Windows Subsystem for Linux), and the source installer, are available at the download site: http://phenix-online.org/download/ Highlights for the 1.21 version of Phenix include: - Likelihood-based docking of models into cryo-EM maps. • Full support for structure determination with AlphaFold models. • New joint X-ray and neutron refinement algorithm. • Quantum Mechanical Restraints (QMR) to calculate ligand restraints in situ. Detailed changes are: - Full support for structure determination with AlphaFold models in Phenix GUI - PredictAndBuild X-ray and Cryo-EM structure solution from data and sequences - Phenix AlphaFold server - Video tutorials for prediction, X-ray structure solution and Cryo-EM map interpretation - Cryo-EM tools support ChimeraX visualization - Cryo-EM density modification and anisotropic scaling display local resolution - Tutorials available for automated structure determination with PredictAndBuild - New em_placement and emplace_local tools - likelihood-based docking of models into cryo-EM maps - MOPAC v22 is now distributed with Phenix - Quantum Mechanical Restraints (QMR) to calculate ligand restraints in situ - Available in phenix.refine and separate command-line tool, mmtbx.quantum_interface - Defaults to MOPAC's PM6-D3H4 - Higher level QM available via 3rd-party Orca package - Restraints - Approximately 27k of 37k restraints (QM calculated and validated) deployed in the GeoStd - Automated tests for programs in the Phenix GUI - ERRASER no longer supported and removed from installation - Remove rebuild_predicted_model (duplicated by predict_and_build) - JSON output added to MolProbity structure validation scripts Please note that this publication should be used to cite the use of Phenix: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD: Acta Cryst. (2019). D75, 861-877. https://doi.org/10.1107/S2059798319011471 Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. The maintenance and distribution of Phenix is funded by the National Institute of General Medical Sciences (NIH) under grant R24-GM141254. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams (he/him/his) Associate Laboratory Director for Biosciences, LBL (https://biosciences.lbl.gov) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, UC Berkeley (http://bioeng.berkeley.edu) Member of the Graduate Group in Comparative Biochemistry, UC Berkeley (http://compbiochem.berkeley.edu) Building 91, Room 410 Building 978, Room 4126 Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: 0000-0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 91R0183 Berkeley, CA 94720, USA. Executive Assistant: Michael Espinosa [ MEEspinosa(a)lbl.gov ][ 1-510-333-6788 ] Phenix Consortium: Ashley Dawn [ AshleyDawn(a)lbl.gov ][ 1-510-486-5455 ] --

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Phenix does not start
by Cygler, Miroslaw 12 Jan '24

12 Jan '24

Hi, I have recently upgraded my MacBook running M1 processor to the Sonoma 14.2.1 operating system. Now, when I tried to start Phenix GUI, a message pops up: “python quit unexpectedly” and guy does not open. Any advice would be helpful. Regards, Mirek

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Secondary structure weights for realspace refinement
by Reza Khayat 11 Jan '24

11 Jan '24

Hi, I hope all is well. Is there a way to alter the weights for secondary structure restraints? Thanks. Best wishes Reza Reza Khayat, PhD City College of New York Associate Professor Department of Chemistry and Biochemistry Co-Director NIH G-RISE program

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Input from the community for panel session: Crystallography is Dead! Long Live Crystallography!
by Nicholas Pearce 02 Jan '24

02 Jan '24

Hello, and happy new year! [and absolutely no apologies for cross-posting 😉] Tomorrow evening, we will have a panel discussion at the CCP4 study weekend about the future of crystallography, called “Crystallography is Dead. Long Live Crystallography!” [https://en.wikipedia.org/wiki/The_king_is_dead,_long_live_the_king]. Whether you’re attending the CCP4SW or not, we want to hear from the community about your thoughts on the subject (see the blurb below), so that we can discuss things the community is most interested in! if you have a few minutes, please do fill in the form (all questions are optional): https://forms.office.com/e/3K5qSMNpYh. Thanks, and looking forward to seeing some of you very soon! Your friendly neighbourhood scientific organisation team, Nicholas Pearce, Helen Ginn, and Clemens Vonrhein Blurb: In this session, we will discuss the current state and the future of crystallographic experiments in the context of structural biology: * what are the unconfronted problems that the field still faces? * what problems are now essentially solved? * where should future method development be focussed? * what challenges are emerging from new experimental developments? * do new experiments provide new perspectives on old problems? Inevitably, this will include discussion of whether these challenges are likely to be addressed by the application of recent advances in AI, and, with the continued developments in cryoEM, what is crystallography's role as a part of the structural biologist's toolbox? Panel Chair: Elspeth Garman Panel Members: Dave Brown, Arwen Pearson, Ashwin Chari Please submit questions for consideration during the panel discussion using the form below! and we look forward to seeing you on 3rd Jan! Some of the questions are asked mischievously - you are welcome to have some fun with your answers! All questions are optional! https://forms.office.com/e/3K5qSMNpYh

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Fwd: Phenix installation on macOS 14 Sonoma
by Billy Poon 01 Jan '24

01 Jan '24

Sorry if this is a duplicate, but I'm not sure if my response got sent to the bulletin board correctly. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org ---------- Forwarded message --------- From: Billy Poon <BKPoon(a)lbl.gov> Date: Sun, Dec 31, 2023 at 6:29 PM Subject: Re: [phenixbb] Phenix installation on macOS 14 Sonoma To: Klureza, Maggie <mklureza(a)g.harvard.edu> Cc: <phenixbb(a)phenix-online.org> Hi Maggie, Can you run the script from inside the sonoma_fix directory? That is, 1) Extract sonoma_fix.tar.gz 2) cd sonoma_fix 3) sudo ./fix_wxpython.sh /Applications/phenix-1.19.2-4158 Inside the sonoma_fix directory, there should be a "bin" directory with conda.exe. The installed versions of Phenix do not come with conda. The fix comes with a standalone version of conda that can modify the Phenix environment with the dependencies. Let us know if it's still not working. Thanks! -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org On Sun, Dec 31, 2023 at 5:49 PM Klureza, Maggie <mklureza(a)g.harvard.edu> wrote: > Hi all, > > Reviving this thread (or trying to, anyway - TBD if I can successfully > reply to a thread begun before I'd joined the phenixbb list!), I recently > updated my Mac OS to 14/Sonoma, and am now also having issues getting > Phenix to work. > > As directed on the installers page > <https://phenix-online.org/download/phenix/release/>, I downloaded the > supplied fix <https://phenix-online.org/download/sonoma_fix.tar.gz>, > extracted the tarball, and ran that code as `sudo > Downloads/sonoma_fix/fix_wxpython.sh /Applications/phenix-1.19.2-4158`. > This was the resulting output/error I got: > > Password: > Removing old version of wxPython > ================================ > Downloads/sonoma_fix/fix_wxpython.sh: line 36: ./bin/conda.exe: No such > file or directory > > Installing new version of wxPython > ================================== > Downloads/sonoma_fix/fix_wxpython.sh: line 42: ./bin/conda.exe: No such > file or directory > > The wxPython package has been updated in /Applications/phenix-1.20.1-4487. > > > Sure enough, when I went to my phenix installation and looked in > conda_base/bin, there was no file named `conda.exe` present. This was true > for both my prior installation (phenix-1.19.2-4158) and when I tried a > newly downloaded version (phenix-1.20.1-4487). > > Can anyone tell me how I get that conda.exe file included with the Phenix > download/how else I might be able to run Phenix with this OS? > > (I sent an email about this to help(a)phenix-online.org before thinking to > hunt through the phenixbb archive, so apologies to whoever checks that > email and is getting this message twice!) > > Many thanks, > Maggie > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org

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Re: [phenixbb] Phenix installation on macOS 14 Sonoma
by Klureza, Maggie 01 Jan '24

01 Jan '24

Hi all, Reviving this thread (or trying to, anyway - TBD if I can successfully reply to a thread begun before I'd joined the phenixbb list!), I recently updated my Mac OS to 14/Sonoma, and am now also having issues getting Phenix to work. As directed on the installers page <https://phenix-online.org/download/phenix/release/>, I downloaded the supplied fix <https://phenix-online.org/download/sonoma_fix.tar.gz>, extracted the tarball, and ran that code as `sudo Downloads/sonoma_fix/fix_wxpython.sh /Applications/phenix-1.19.2-4158`. This was the resulting output/error I got: Password: Removing old version of wxPython ================================ Downloads/sonoma_fix/fix_wxpython.sh: line 36: ./bin/conda.exe: No such file or directory Installing new version of wxPython ================================== Downloads/sonoma_fix/fix_wxpython.sh: line 42: ./bin/conda.exe: No such file or directory The wxPython package has been updated in /Applications/phenix-1.20.1-4487. Sure enough, when I went to my phenix installation and looked in conda_base/bin, there was no file named `conda.exe` present. This was true for both my prior installation (phenix-1.19.2-4158) and when I tried a newly downloaded version (phenix-1.20.1-4487). Can anyone tell me how I get that conda.exe file included with the Phenix download/how else I might be able to run Phenix with this OS? (I sent an email about this to help(a)phenix-online.org before thinking to hunt through the phenixbb archive, so apologies to whoever checks that email and is getting this message twice!) Many thanks, Maggie

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geometrical restraints between symmetry related chains
by Jorge Iulek 30 Dec '23

30 Dec '23

Dear all, I am working currently on a structure that should be "peptide bond" between chains, but the "second" part of the chain is in a symmetry related peer. Numbering is continuous and there are justifications to why the chains are separately named with different chain ID's. By the way, this "connection" is "full of glycines" so a kind of flexible, but a continuous stretch can be seen at "reasonable" density (and despite low resolution). To better explain, say I have chain C residue x to be bound to chain K, at symm operation -x-1,y-1/2,-z-1/2, residue x + 1. I would prefer to really refine the presence of these "connecting" glycines, of course with due geometrical restraints imposed (precious at this low resolution). phenix.refine offers: refinement.geometry_restraints.edits at bond with the possibility to indicate the symmetry_operation for the "second atom" within the bond. But this "symmetry_operation" indication is not available (?) for the other geometry_restraints edits, like angle, dihedral, etc. (eventually, planarity might also make easier). Do I miss anything here? Currently, I see 3 possibilities: a) somehow (how?) I can add angle, dihedral restraints in involving chains in symmetry related operations b) I bring the symmetry related chain to its non "symmetry related" position and change chains names/residues ID, etc., so I go into this go/return of naming at each step of the refinement work/analysis c) I add "extra" ( + - like alternate conformation residues) residues to each end of the connection, such that these extra residues will receive due conventional geometrical restraints (as phenix.refine does for contiguous residues in a chain) but I force them to be on the same position (and probably declare 0.5 occupancy for these overlying residues). "a" should be the easiest, if available somehow; "b" would be cumbersome during the refinement/analysis process; "c" seems to be the most complex but maybe the best if it works. Nevertheless, someone might have an easier suggestion. Thanks, Jorge

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Phenix windows distortion windows
by Dmitry Semchonok 28 Dec '23

28 Dec '23

Dear colleagues, I am not sure of the reason, but when I run Phenix, I get the following distortion of the Phenix window. Then, the distortion disappears if I move the cursor somewhere else and click somewhere out of the Phenix window. (please see attachment) Do you know the reasons and how to fix that? Phenix version - 1.21-5187 WSL Windows 11 I will try to 1. roll-back windows drivers 2. update Phenix Kind regards, Dmitry

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Re: [phenixbb] phenixbb Digest, Vol 216, Issue 7 (out of office)
by Elisabeth Laurent 28 Dec '23

28 Dec '23

Thank you for your e-mail. I am out of office until January 2nd, 2024. I will respond to your e-mail as soon as possible upon my return. For urgent matters please contact: bmca(a)boku.ac.at Thank you for your understanding. With kind regards, Elisabeth Laurent >>> <phenixbb-request(a)phenix-online.org> 27.12.23 17:32 >>> Send phenixbb mailing list submissions to phenixbb(a)phenix-online.org To subscribe or unsubscribe via the World Wide Web, visit http://phenix-online.org/mailman/listinfo/phenixbb or, via email, send a message with subject or body 'help' to phenixbb-request(a)phenix-online.org You can reach the person managing the list at phenixbb-owner(a)phenix-online.org When replying, please edit your Subject line so it is more specific than "Re: Contents of phenixbb digest..." Today's Topics: 1. Re: phenix.model_vs_sequence not working as expected (Oleg Sobolev) 2. real space refinement of the model in cryo-EM map (Dmitry Semchonok) 3. Re: real space refinement of the model in cryo-EM map (Pavel Afonine) ---------------------------------------------------------------------- Message: 1 Date: Fri, 22 Dec 2023 11:21:13 -0800 From: Oleg Sobolev <osobolev(a)lbl.gov> To: "Tanner, John J." <TannerJJ(a)missouri.edu> Cc: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Subject: Re: [phenixbb] phenix.model_vs_sequence not working as expected Message-ID: <CADd3otGkgta4heL2mHYB1sfkm_AxEw77Psd7RdS+pGQhjED7dA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi John, Thank you for reporting the issue. I have fixed it. This tool should work again in Phenix builds starting from 5188. Best regards, Oleg Sobolev. On Wed, Dec 20, 2023 at 9:35?AM Tanner, John J. <TannerJJ(a)missouri.edu> wrote: > I?ve noticed that command line phenix.model_vs_sequence does not work in > phenix-1.21rc1-5156. > > > > Here?s the data: > > > > [tannerjj@dizzy pdbs]$ which phenix.model_vs_sequence > > /linux/src/phenix-1.21rc1-5156/build/bin/phenix.model_vs_sequence > > [tannerjj@dizzy pdbs]$ phenix.model_vs_sequence 8DKP.pdb > ../depo/8DKP.fasta > > Traceback (most recent call last): > > File > "/linux/src/phenix-1.21rc1-5156/build/../modules/cctbx_project/mmtbx/command_line/model_vs_sequence.py", > line 75, in <module> > > run(sys.argv[1:]) > > File > "/linux/src/phenix-1.21rc1-5156/build/../modules/cctbx_project/mmtbx/command_line/model_vs_sequence.py", > line 48, in run > > pdb_in = iotbx.pdb.inpu(params.input.pdb_file) > > AttributeError: 'module' object has no attribute 'inpu' > > > > > > It worked fine in phenix-1.20.1-4487: > > > > [tannerjj@dizzy pdbs]$ source /linux/src/phenix-1.20.1-4487/phenix_env.csh > > [tannerjj@dizzy pdbs]$ which phenix.model_vs_sequence > > /linux/src/phenix-1.20.1-4487/build/bin/phenix.model_vs_sequence > > [tannerjj@dizzy pdbs]$ phenix.model_vs_sequence 8DKP.pdb > ../depo/8DKP.fasta > > Skipping non-polymer chain 'A' > > Skipping non-polymer chain 'B' > > Skipping non-polymer chain 'A' > > Skipping non-polymer chain 'B' > > Chain 'A': > > best matching sequence: 8DKP_1|Chains > > sequence identity: 100.00% > > 10 residue(s) missing from PDB chain (3 at start, 1 at end) > > 1 gap(s) in chain > > > > > > PDB file ---QSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRGKHXXXXX > > > |||||||||||||||||||||||||||||||||||||||||||||||||||| > > > sequence SRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRGKHSGSGS > > > > > PDB file XGSXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX > > > || > > > sequence SGS--------------------------------------------------------- > > > > > PDB file XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXMMGEQFVTGETIREA > > > ||||||||||||||| > > > sequence ---------------------------------------------MMGEQFVTGETIREA > > > > > PDB file LKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGIYEGPGISI > > > |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| > > > sequence LKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGIYEGPGISI > > > > > PDB file KLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLC > > > |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| > > > sequence KLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLC > > > > > PDB file LDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWDAEIKRAQLD > > > |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| > > > sequence LDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWDAEIKRAQLD > > > > > PDB file GLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYHMAGKDFHVGKY > > > |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| > > > sequence GLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYHMAGKDFHVGKY > > > > > PDB file EFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRLLENGANSSFVHRIN > > > |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| > > > sequence EFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRLLENGANSSFVHRIN > > > > > PDB file DPKVSIDELIADPVEVV- > > ||||||||||||||||| > > sequence DPKVSIDELIADPVEVVR > > > > Chain 'B': > > best matching sequence: 8DKP_1|Chains > > sequence identity: 100.00% > > 8 residue(s) missing from PDB chain (0 at start, 1 at end) > > 1 gap(s) in chain > > > > > > PDB file SRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRGKHXXXXX > > > ||||||||||||||||||||||||||||||||||||||||||||||||||||||| > > > sequence SRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRGKHSGSGS > > > > > PDB file XXSXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX > > > | > > > sequence SGS--------------------------------------------------------- > > > > > PDB file XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXMMGEQFVTGETIREA > > > ||||||||||||||| > > > sequence ---------------------------------------------MMGEQFVTGETIREA > > > > > PDB file LKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGIYEGPGISI > > > |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| > > > sequence LKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGIYEGPGISI > > > > > PDB file KLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLC > > > |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| > > > sequence KLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLC > > > > > PDB file LDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWDAEIKRAQLD > > > |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| > > > sequence LDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWDAEIKRAQLD > > > > > PDB file GLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYHMAGKDFHVGKY > > > |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| > > > sequence GLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYHMAGKDFHVGKY > > > > > PDB file EFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRLLENGANSSFVHRIN > > > |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| > > > sequence EFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRLLENGANSSFVHRIN > > > > > PDB file DPKVSIDELIADPVEVV- > > ||||||||||||||||| > > sequence DPKVSIDELIADPVEVVR > > > > [tannerjj@dizzy pdbs]$ > > > > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org >

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real space refinement of the model in cryo-EM map
by Dmitry Semchonok 28 Dec '23

28 Dec '23

Dear colleagues, Does anyone know how to improve the Ramachandran plot Z score (Rama-Z)? Ours seems to be too good (low) 🙂 Is there any cure in Phenix for that? Maybe changing certain parameters/restraints can aid? Thank you. Kind regards, Dmitry

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phenix.model_vs_sequence not working as expected
by Tanner, John J. 23 Dec '23

23 Dec '23

I’ve noticed that command line phenix.model_vs_sequence does not work in phenix-1.21rc1-5156. Here’s the data: [tannerjj@dizzy pdbs]$ which phenix.model_vs_sequence /linux/src/phenix-1.21rc1-5156/build/bin/phenix.model_vs_sequence [tannerjj@dizzy pdbs]$ phenix.model_vs_sequence 8DKP.pdb ../depo/8DKP.fasta Traceback (most recent call last): File "/linux/src/phenix-1.21rc1-5156/build/../modules/cctbx_project/mmtbx/command_line/model_vs_sequence.py", line 75, in <module> run(sys.argv[1:]) File "/linux/src/phenix-1.21rc1-5156/build/../modules/cctbx_project/mmtbx/command_line/model_vs_sequence.py", line 48, in run pdb_in = iotbx.pdb.inpu(params.input.pdb_file) AttributeError: 'module' object has no attribute 'inpu' It worked fine in phenix-1.20.1-4487: [tannerjj@dizzy pdbs]$ source /linux/src/phenix-1.20.1-4487/phenix_env.csh [tannerjj@dizzy pdbs]$ which phenix.model_vs_sequence /linux/src/phenix-1.20.1-4487/build/bin/phenix.model_vs_sequence [tannerjj@dizzy pdbs]$ phenix.model_vs_sequence 8DKP.pdb ../depo/8DKP.fasta Skipping non-polymer chain 'A' Skipping non-polymer chain 'B' Skipping non-polymer chain 'A' Skipping non-polymer chain 'B' Chain 'A': best matching sequence: 8DKP_1|Chains sequence identity: 100.00% 10 residue(s) missing from PDB chain (3 at start, 1 at end) 1 gap(s) in chain PDB file ---QSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRGKHXXXXX |||||||||||||||||||||||||||||||||||||||||||||||||||| sequence SRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRGKHSGSGS PDB file XGSXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX || sequence SGS--------------------------------------------------------- PDB file XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXMMGEQFVTGETIREA ||||||||||||||| sequence ---------------------------------------------MMGEQFVTGETIREA PDB file LKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGIYEGPGISI |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| sequence LKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGIYEGPGISI PDB file KLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLC |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| sequence KLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLC PDB file LDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWDAEIKRAQLD |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| sequence LDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWDAEIKRAQLD PDB file GLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYHMAGKDFHVGKY |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| sequence GLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYHMAGKDFHVGKY PDB file EFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRLLENGANSSFVHRIN |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| sequence EFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRLLENGANSSFVHRIN PDB file DPKVSIDELIADPVEVV- ||||||||||||||||| sequence DPKVSIDELIADPVEVVR Chain 'B': best matching sequence: 8DKP_1|Chains sequence identity: 100.00% 8 residue(s) missing from PDB chain (0 at start, 1 at end) 1 gap(s) in chain PDB file SRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRGKHXXXXX ||||||||||||||||||||||||||||||||||||||||||||||||||||||| sequence SRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRGKHSGSGS PDB file XXSXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX | sequence SGS--------------------------------------------------------- PDB file XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXMMGEQFVTGETIREA ||||||||||||||| sequence ---------------------------------------------MMGEQFVTGETIREA PDB file LKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGIYEGPGISI |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| sequence LKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGIYEGPGISI PDB file KLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLC |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| sequence KLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLC PDB file LDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWDAEIKRAQLD |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| sequence LDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWDAEIKRAQLD PDB file GLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYHMAGKDFHVGKY |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| sequence GLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYHMAGKDFHVGKY PDB file EFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRLLENGANSSFVHRIN |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| sequence EFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRLLENGANSSFVHRIN PDB file DPKVSIDELIADPVEVV- ||||||||||||||||| sequence DPKVSIDELIADPVEVVR [tannerjj@dizzy pdbs]$

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Two-year postdoctoral position in time-resolved crystallography at IBS in Grenoble
by Elke De Zitter 22 Dec '23

22 Dec '23

Dear all, We have an immediate opening for a two-year postdoctoral researcher in SNaX team of the DYNAMOP group at the Institute for Structural Biology in Grenoble (France). The successful candidate will work on the development and optimization of bio-scavengers towards toxic organophosphorus compounds. To attain this goal, the researcher will use time-resolved crystallography and in silico protein design methods. The position is funded by the French National Research Agency via the University Grenoble Alpes, and is open for a young researcher. Applicants must have obtained a Ph.D. in structural biology, biochemistry, biophysics, physics, chemistry, or a related field, no more than two years before the start of the project. The candidate must show a track-record of publications in peer-reviewed journals, and is expected to be proficient in English and highly motivated to learn new skills. The candidate will work in the multidisciplinary DYNAMOP group and thus needs to be a good team player as well as being capable of working independently. While the research will be carried out in English, non-French-speaking candidates are expected to learn the basics of French in order to facilitate communication and integration into the laboratory. Experience with one or more of the following skills would be highly evaluated: protein design or the usage of artificial intelligence for structural biology, protein expression and purification, protein crystallization and macromolecular crystallography, serial crystallography, programming or scripting. Interested candidates can apply via [ https://emploi.univ-grenoble-alpes.fr/offres/doctorants/postdoctoral-resear… | https://emploi.univ-grenoble-alpes.fr/offres/doctorants/postdoctoral-resear… ] . We advice to contact Elke De Zitter ( elke.de-zitter(a)ibs.fr ) to obtain more information about the postdoctoral position and application procedure. All the best, Elke Elke De Zitter Institut de Biologie Structurale - IBS group DYNAMOP 71 avenue des Martyrs 38044 Grenoble Cedex 9, France +33 4 57 42 86 56 elke.de-zitter(a)ibs.fr

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unassigned densities
by Dmitry Semchonok 18 Dec '23

18 Dec '23

Dear colleagues, Is there a way to assign cryo-EM densities not included in the model sequence? Do you have any tools that can help? More closely, is there a way to screen the cryo-EM map + model, point out the unassigned densities, and provide the possible structures to fit in (e.g., water molecules, etc.)? Thank you. Kind regards, Dmitry

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math behind beamstop_shadow_outliers
by Gao, Yunyun 14 Dec '23

14 Dec '23

Hi everyone, While I can find references for other outlier rejection options in scaling.outlier_rejction, there is none for beamstop_shadow_outliers. I am wondering what is the math behind z_lim_ac and z_lim_c. Another question would be: Does the same criteria also apply for the medium-resolution (e.g. 6-8 A) reflections? (like reflections under the beamstop support) Thanks! Best regards, Yunyun ------------------------------------ Yunyun Gao, Dr HARBOR Universitaet Hamburg Tel +49 (0)40 42838-3685

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Bug in optimize weights
by Mark Saper 08 Dec '23

08 Dec '23

I am running build 5156 on macOS 13.6.1. I am refining a multi-molecule with imperfect NCS. When I tried to use "Optimize X-ray/sterochemistry" and "Optimize X-ray/ADP weight” the program aborted with an error during the first cycle. The error was: ====================== XYZ individual (reciprocal space) ====================== AttributeError I submitted a bug report via the internal bug report system. I would appreciate how to get around this problem. Should I try the previous stable version? Many thanks, Mark _____________________ Mark A. Saper, Ph.D. Visiting Professor Dept of Microbiology and Molecular Genetics Hebrew University Faculty of Medicine Associate Professor Emeritus of Biological Chemistry University of Michigan Medical School saper(a)umich.edu <mailto:[email protected]> | +972 52 815-0480

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Reference model problem
by Luca Pellegrini 07 Dec '23

07 Dec '23

I am trying to use a reference model in real_space_refinement, but phenix stops with the message: “Cannot not restrain working model to self and a reference model simultaneously” (see below). The reference and working models are identical but bound to different ligands. As far as a I can see, all I am doing is adding the reference model in the input window and ticking the box for reference model restraints (phenix 1.21rc1-4985). Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA UK [cid:[email protected]]

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Error 1.21rc1-5156 macOS and cross special position
by Xavier Brazzolotto 02 Dec '23

02 Dec '23

Dear Phenix developers, I have recently updated to macOS Sonoma and updated Phenix to the latest RC (1.21rc1-5156). I do have recent data where a residue gets a bit too close to its symmetric mate. In order to be able to start the refinement, I have to select the model interpretation option « allow_polymer_cross_special_position=True » In this case, the refinement process starts and does my 3 refinement cycles. However, the UI gives me a final error message stating that I have to enable the « cross-special position » (which is already True). The refined data are present (pdb, mtz, log, cif, eff, geo) but I do not get any analysis on these data. No _info.txt, no .kin files. The log ends with a « Sorry » If I deliberately move the faulty residue a bit out of its position (no more clashing with its symmetric mate) and NOT allow the cross-special position, then the refinement ends well with the correct final data analysis. Not a big deal per se, but but I suspect a small issue in the initiation of the analysis programs (Molprobity / King / etc…). Xavier

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Re: [phenixbb] CCP4 Study Weekend 2024 - Early bird registration including standard student bursary deadline coming soon!
by Karen McIntyre - STFC UKRI 01 Dec '23

01 Dec '23

Dear all, Registration is open for the 2024 CCP4 study weekend entitled "Decision making in MX - how to be a productive structural biologist". This year we are focusing on decision-making in macromolecular crystallography: when to use what automated tool, how to interpret the output and when you need to get your hands dirty instead. The frontiers of crystallography now involve massive multi-crystal and multi-dimensional experiments. This means the more that you can leave to the automated pipelines, the more you can focus on the novel elements of your experiment. Sometimes those automated tools work, and sometimes they fail (but have maybe not told you exactly why or how). Sometimes they don't even exist. In that case, how can you return to the basics and develop new strategies to break down the barriers to publication? Once again, this year the CCP4 Study Weekend will be held as a hybrid event from the 3rd to 5th January 2024, enabling people to choose whether to attend in-person or virtually. The in-person event will be held at the East Midlands Conference Centre, Nottingham, UK. We would like to invite you to another iteration of the ever-popular CCP4 Study Weekend - to start the year 2024 with a lot of fresh ideas, new insights and (hopefully) new friends and contacts to boost. As always it will be an eclectic mix of bleeding-edge science, in-depth presentations, discussion panel, poster-sessions, hands-on tutorials and plenty of opportunities for social interactions including the ceilidh. For full details, programme, logistics and registration, please visit the Study Weekend website<https://studyweekend.ccp4.ac.uk/>. Important Key Dates: * Early bird registration final date: 19 November 2023; * Standard Student bursaries are open to all students registering during early bird period i.e. now until 19 November which cover the cost of registration plus one night accommodation; * Registration for in-person delegates closes 4 December 2023 (or earlier if in-person places sell out although you will be able to join the in-person waitlist). We hope to see you there! Scientific Organisers: Helen Ginn (Deutsches Elektronen-Synchrotron, DESY, Germany) Nick Pearce (Linköping University, Sweden) Clemens Vonrhein (Global Phasing Ltd, UK) Administrative Organisers: Karen McIntyre (CCP4, UK)

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The experiment is still very much needed (though AlphaFold helps a lot)
by Tom Terwilliger 01 Dec '23

01 Dec '23

Hi Structural biologist colleagues! Our article that helps you make the case that the experiment is still very much needed is now out: https://www.nature.com/articles/s41592-023-02087-4 "AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination." Nature Methods (2023) Also, here is a video on the Phenix Tutorials YouTube channel that describes this analysis: https://www.youtube.com/watch?v=ugMPYdPo8Bc (I hope you will be happy to see that you and your structural biology colleagues get the credit for making AlphaFold possible at 2:35 in the introduction of this video! Keep up the fantastic structural biology work!) All the best, Tom T -- Thomas C Terwilliger Laboratory Fellow, Los Alamos National Laboratory Senior Scientist, New Mexico Consortium 100 Entrada Dr, Los Alamos, NM 87544 Email: tterwilliger(a)newmexicoconsortium.org Tel: 505-431-0010

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Possible problem with eLBOW in version 1.21rc1.5058 using smiles string
by Francisco Javier Medrano 30 Nov '23

30 Nov '23

Dear developers: I have tried to use eLBOW in version 1.21rc1.5058 to generate a cif file for a ligand and the program give me the following error: SMILES parser error:"Unable to load parsing table". The smiles string used was OP(OP(O)(O)=O)(O)=O, but it does not work for other strings. It does work if you supply a pdb file with connect records. If I use version 1.20.1-4487 with the same smiles string it does work properly. Is there any bur in the 1.21 version? Best regards -- Fº Javier Medrano Cristalografía de Macromoléculas Centro de Investigaciones Biológicas Margarita Salas C/ Ramiro de Maeztu, nº 9 Madrid - Spain

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issue with restrains
by Dmitry Semchonok 22 Nov '23

22 Nov '23

Dear colleagues, The issue with the refinement (Phenix 1.21rc1-5130) The refinement does not recognize the phil parameters prepared with ReadySet. [cid:5bb12054-9715-417b-a68d-58c1228ffe56] Please prompt me on how to proceed. Thank you Kins regards, Dmitry

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Errors in atomic coordinates and B factors in MX
by John R Helliwell 21 Nov '23

21 Nov '23

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Question about phenix.resolve_cryo_em
by Reza Khayat 20 Nov '23

20 Nov '23

Hi, Is it possible to turn off the model refinement procedure in phenix.resolve.cryo_em and go straight into density modification? My current model fits reasonably well. Also, Does the routine work well with nucleic acid (e.g. something like RNA from ribosome)? Best wishes, Reza

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EM difference map calculation
by Leonid Sazanov 14 Nov '23

14 Nov '23

Hi, I have tried to use this command in 1.21rc1-4933: phenix.real_space_diff_map XXX.pdb XXX_box.ccp4 resolution=3.0 Model was real-space refined against _box map and the result with map_model_difference_1.ccp4 looks more or less as expected, except that at medium to low density levels strong cubic shape artifacts start to appear. I thought that might be because _box.ccp4 map is not cubic, but re-running with the original cubic map gives even stronger artifacts. Is this a known issue and how this might be resolved? Or perhaps this functionality now comes in one of the newer tools? Many thanks! Leonid -- Prof. Leonid Sazanov FRS IST Austria Am Campus 1 A-3400 Klosterneuburg Austria Phone: +43 2243 9000 3026 E-mail: sazanov(a)ist.ac.at

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Exclude Waters from order_solvent=true updates
by Schulz, Dr. Eike 14 Nov '23

14 Nov '23

Hello everyone, I am refining a few structures via a bash script using constrained occupancy refinement by providing a parameter file. I am trying to model the occupancy of a ligand and the water molecules in its vicinity. This works generally well, but as soon as I switch on ordered_solvent=true, these water molecules are also filtered / updated and eventually removed. How can I avoid this ? That is specifically excluding a number of water molecules from being updated ? With best regards, Eike

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Automated estimation of voxel size using reference pixel size in phenix?
by Oliver Clarke 14 Nov '23

14 Nov '23

Hi, In cryoEM, the pixel size is often not known with certainty, and we need to calibrate it by measuring the real space correlation of a reference crystal structure of a component at different nominal pixel sizes. Currently we do this manually, using `fitmap` in UCSF Chimera, but given the sophisticated set of tools in Phenix for fitting atomic models and analyzing real space correlations, I was wondering if a tool in Phenix already exists to do this, or whether there would be any interest in adding such a tool at some point? Cheers Oli

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an atom moves away during model refinement
by Dmitry Semchonok 07 Nov '23

07 Nov '23

Dear colleagues, While refining my model, the Mg atom for some of the margin units moves far away from them. I am also using the ELBOW files of Mg during the refinement. What is the way to restrict the movement of atoms during refinement? I found that this behaviour can be observed after simulated annealing is on. And the harmonic_restraints may be acquired to restrict atom movement. Is that right? I am using the GUI version of Phenix, and I cannot see those parameters. Thank you. Sincerely, Dmitry

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phenix.real_space_diff_map - difference between output maps
by Jose Artur Brito 31 Oct '23

31 Oct '23

Dear All, I am trying to use phenix.real_space_diff_map to assess "reminiscent" density in a 1.9 A cryoEM map. Can someone explain the difference between map_model_difference_1.ccp4 and map_model_difference_2.ccp4 that PHENIX outputs? Thanks in advance, best, Jose --

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Re: [phenixbb] Pb LocalResolutionMap calculation
by CUNIASSE Philippe 31 Oct '23

31 Oct '23

Hi Tom, i dowloaded and installed the nightly builds 1.21rc1-5134 but i do not see a direct access to the n_boxes parameter in the gui of the local Resolution Map menu. Is that normal, is it in the previous nightly build (5133)? Another question : in the gui of the local Resolution Map menu, i can see the value of the parameters by navigating the parameters menu, but i cannot modified their values. Is that normal an how to solve it ? Thank you so much for your help. Best regards. Philippe. ________________________________ De : phenixbb-bounces(a)phenix-online.org <phenixbb-bounces(a)phenix-online.org> de la part de CUNIASSE Philippe Envoyé : dimanche 29 octobre 2023 22:06:55 À : Tom Terwilliger Cc : phenixbb(a)phenix-online.org Objet : [PROVENANCE INTERNET] Re: [phenixbb] Pb LocalResolutionMap calculation Hi Tom, Thank you so much. I will test some values of this n_boxes parameter. Best regards. Philippe. ________________________________ De : Tom Terwilliger <tterwilliger(a)newmexicoconsortium.org> Envoyé : dimanche 29 octobre 2023 14:03:45 À : CUNIASSE Philippe Cc : phenixbb(a)phenix-online.org; Tom Terwilliger Objet : Re: [phenixbb] Pb LocalResolutionMap calculation Hi Philippe, Yes, certainly the number of boxes affects the resulting local_resolution map. The 2400 boxes correspond to 14x14x14 boxes for a cubic map which means that you have only a gradual sampling along any axis of your map. You can adjust the number of boxes with the parameter n_boxes=2400. In the GUI, search under "All parameters" for "box" and you'll get the entry form. I will move this to the front page in tomorrow's nightly build of Phenix so it is easier to set. All the best, Tom T On Sun, Oct 29, 2023 at 3:42 AM CUNIASSE Philippe <Philippe.CUNIASSE(a)cea.fr<mailto:[email protected]>> wrote: Hi Tom, thank so much you for your answer. I uploaded the nigthtly build and it worked far better (a couple of hours) and ended correctly. I noticed that the gain was due to the fact the only about 2400 boxes were calculated (in place of more than 40000 in my slow previous calculation, likely explaining the gain of a factor 20). As i have a very large map, i wonder how this affects the quality of the LocalResolutionMap. And i also wonder if there is a mean to define this parameter to study this effect. Thank you so much for your help. Best regards. Philippe. ----------------------------------------------- Philippe Cuniasse, PhD/HDR. Institut de Biologie Integrative de la cellule. UMR 9198 CNRS-CEA-Univ Paris Sud Bat 144 CE-Saclay 91191 Gif-sur-Yvette Cedex France Tel: (33) 1 69 08 56 35 Fax: (33) 1 69 08 47 12 Email: philippe.cuniasse(a)cea.fr<mailto:[email protected]> Web: http://biodev.cea.fr/rasmot3d/ ----------------------------------------------- ________________________________ De : Tom Terwilliger <tterwilliger(a)newmexicoconsortium.org<mailto:[email protected]>> Envoyé : vendredi 27 octobre 2023 11:04:52 À : CUNIASSE Philippe Cc : phenixbb(a)phenix-online.org<mailto:[email protected]>; Tom Terwilliger Objet : Re: [phenixbb] Pb LocalResolutionMap calculation Hi Philippe, I'm sorry for the slow calculation...the problem is the number of boxes is too high. If you download a nightly build like this one: https://phenix-online.org/download/phenix/nightly/?version=1.21rc1-5130 then it should be a lot faster (still not quick, but in your case should be 20x faster). All the best, Tom T On Fri, Oct 27, 2023 at 2:16 AM CUNIASSE Philippe <Philippe.CUNIASSE(a)cea.fr<mailto:[email protected]>> wrote: Dear all, i try to calculate local resolution maps with phenix since a couple of days. It turns out that the calculation seems very slow and i suspect that there is a problem because i even cannot stop the calculation with the abort button in the gui. In my last run (still running), i use 2 half-maps and the program can read them correctly, start the calculation by returning that 42875 boxes are considered. I run it on my MacBook pro (M1 running OSX 13.4 with 32Gb RAM) on 4 cpu. The calculation actually runs on 4 CPUs. However, with this calculation (and also a smaller map with about 17000 boxes on 1CPU), the calculations run more than 24 hours without finishing. I wonder if there coud be a problem and if no, what could be the duration of such calculation. Thanks in advance for your help. Best regards. Philippe Cuniasse. ----------------------------------------------- Philippe Cuniasse, PhD/HDR. Institute for Integrative Biology of the Cell (I2BC) UMR 9198 CNRS-CEA-Univ Paris Sud Bat 144 CE-Saclay 91191 Gif-sur-Yvette Cedex, France Tel: (33) 1 69 08 56 35 Fax: (33) 1 69 08 47 12 Email: philippe.cuniasse(a)cea.fr<mailto:[email protected]> Web: http://biodev.cea.fr/rasmot3d/ Web: https://www.i2bc.paris-saclay.fr [signature_2661676233] ----------------------------------------------- _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: phenixbb-leave(a)phenix-online.org<mailto:[email protected]> -- Thomas C Terwilliger Laboratory Fellow, Los Alamos National Laboratory Senior Scientist, New Mexico Consortium 100 Entrada Dr, Los Alamos, NM 87544 Email: tterwilliger(a)newmexicoconsortium.org<mailto:[email protected]> Tel: 505-431-0010 -- Thomas C Terwilliger Laboratory Fellow, Los Alamos National Laboratory Senior Scientist, New Mexico Consortium 100 Entrada Dr, Los Alamos, NM 87544 Email: tterwilliger(a)newmexicoconsortium.org<mailto:[email protected]> Tel: 505-431-0010

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Pb LocalResolutionMap calculation
by CUNIASSE Philippe 30 Oct '23

30 Oct '23

Dear all, i try to calculate local resolution maps with phenix since a couple of days. It turns out that the calculation seems very slow and i suspect that there is a problem because i even cannot stop the calculation with the abort button in the gui. In my last run (still running), i use 2 half-maps and the program can read them correctly, start the calculation by returning that 42875 boxes are considered. I run it on my MacBook pro (M1 running OSX 13.4 with 32Gb RAM) on 4 cpu. The calculation actually runs on 4 CPUs. However, with this calculation (and also a smaller map with about 17000 boxes on 1CPU), the calculations run more than 24 hours without finishing. I wonder if there coud be a problem and if no, what could be the duration of such calculation. Thanks in advance for your help. Best regards. Philippe Cuniasse. ----------------------------------------------- Philippe Cuniasse, PhD/HDR. Institute for Integrative Biology of the Cell (I2BC) UMR 9198 CNRS-CEA-Univ Paris Sud Bat 144 CE-Saclay 91191 Gif-sur-Yvette Cedex, France Tel: (33) 1 69 08 56 35 Fax: (33) 1 69 08 47 12 Email: philippe.cuniasse(a)cea.fr<mailto:[email protected]> Web: http://biodev.cea.fr/rasmot3d/ Web: https://www.i2bc.paris-saclay.fr [signature_2661676233] -----------------------------------------------

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an installation issue
by Dmitry Semchonok 27 Oct '23

27 Oct '23

Dear colleagues, Installing phenix of WSL I received an error - david@DESKTOP-NMD1JP9:~$ phenix [1] 402 david@DESKTOP-NMD1JP9:~$ Error in sys.excepthook: Traceback (most recent call last): File "/usr/local/phenix-1.21rc1-5130/modules/phenix/wxGUI2/App.py", line 961, in _excepthook Error.show_exception_dialog(type, value, traceback) File "/usr/local/phenix-1.21rc1-5130/modules/phenix/wxGUI2/Error.py", line 76, in show_exception_dialog if (app.bug_timer.IsRunning() is False): AttributeError: 'PhenixApp' object has no attribute 'bug_timer' Original exception was: Traceback (most recent call last): File "/usr/local/phenix-1.21rc1-5130/build/../modules/phenix/wxGUI2/command_line/main.py", line 34, in <module> run(sys.argv[1:]) File "/usr/local/phenix-1.21rc1-5130/build/../modules/phenix/wxGUI2/command_line/main.py", line 28, in run wxapp = App.PhenixApp(args) File "/usr/local/phenix-1.21rc1-5130/modules/phenix/wxGUI2/App.py", line 84, in __init__ wx.App.__init__(self, 0) File "/usr/local/phenix-1.21rc1-5130/conda_base/lib/python2.7/site-packages/wx-3.0-gtk2/wx/_core.py", line 8628, in __init__ self._BootstrapApp() File "/usr/local/phenix-1.21rc1-5130/conda_base/lib/python2.7/site-packages/wx-3.0-gtk2/wx/_core.py", line 8196, in _BootstrapApp return _core_.PyApp__BootstrapApp(*args, **kwargs) File "/usr/local/phenix-1.21rc1-5130/modules/phenix/wxGUI2/App.py", line 118, in OnInit show_splash_screen(timeout=2000) File "/usr/local/phenix-1.21rc1-5130/modules/phenix/wxGUI2/App.py", line 1015, in show_splash_screen dlg,-1,citations.format_citation(citations.citations_db.get("phenix"))) File "/usr/local/phenix-1.21rc1-5130/conda_base/lib/python2.7/site-packages/wx-3.0-gtk2/wx/_controls.py", line 997, in __init__ _controls_.StaticText_swiginit(self,_controls_.new_StaticText(*args, **kwargs)) UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 40: ordinal not in range(128) 1. it is a new Desktop and WSL; 2. Additionally, I installed python 3. I run sudo locale-gen "en_GB.UTF-8" (but maybe there is a command to check if it works properly) 4. on my laptop WSL phenix works nicely Any advice? Many thanks. Sincerely, Dmitry

2 1

Apply NFC operators to helical structure
by Dmitry Semchonok 23 Oct '23

23 Oct '23

Dear colleagues, Please prompt me on correctly applying the symmetry parameters to the helical cryo-em map. What I did: 1. Found symmetry with Map symmetry. The process finished successfully. 2. Applied the NFC operators. But the outcome has only two units (C2 symmetry). When I put more units in the program setting, nothing happens after the run; moreover, the output is not generated. Could you please advise how to fill the helical cryo-EM structure with units? Many thanks for considering my request. Sincerely, Dmitry

2 1